Hello, yes, that's right. We've all seen guanidinium groups parallel with aromatic rings and shielding them from solvent. I think it might approach that sort of arrangement in this case. Cheers, Jon.C.
Sent from ProtonMail mobile -------- Original Message -------- On 1 Feb 2022, 16:52, Krieger, James M wrote: > Probably arginine and tyrosine do like each other a fair bit. They can form > both cation-pi interactions and hydrogen bonds. > Best wishes > James > >> On 1 Feb 2022, at 16:41, Jon Cooper >> <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Hello, I did wonder if it might be an alternative conformation for the >> quanidinium group of that nearby arginine. Being such high resolution, quite >> low occupancy groups would show up, I think, but it may just be too far away >> and I don't know how much tyrosine and arginine like each other! >> >> Sent from ProtonMail mobile >> >> -------- Original Message -------- >> On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote: >> >>> Thank you for your suggestions. >>> As this is a high resolution structure (1.1Å) I have been refining it with >>> anisotropic B-factors. >>> Placing a propionate or modelling a phosphate at this position blows up >>> during the refinement. >>> I will inform you if I am successful in figuring this out. >>> >>> Best >>> Misbha >>> >>> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William >>> <william.shep...@synchrotron-soleil.fr> wrote: >>> >>>> Dear Misba, >>>> >>>> Perhaps it's a silly question, but have you tried to model in propionate? >>>> The carboxylate group could make H-bonds to both the Arginine sidechain >>>> and the the tyrosine OH group. Propionate should show no anomalous signal. >>>> >>>> Just my 2-bits worth. >>>> >>>> Cheers, >>>> Bill >>>> >>>> ----- Original Message ----- >>>> From: "Gerard Bricogne" <g...@globalphasing.com> >>>> To: CCP4BB@JISCMAIL.AC.UK >>>> Sent: Saturday, 29 January, 2022 18:34:26 >>>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification >>>> >>>> Dear Misba, >>>> >>>> Thank you for your reply and for the very clear picture. I hope you >>>> will be able to share the result once the mystery is solved. >>>> >>>> With best wishes, >>>> >>>> Gerard. >>>> >>>> -- >>>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote: >>>>> Dear Gerard, >>>>> The data were collected at 0.966Å and I can see the anomalous peaks for As >>>>> at Cysteines which are modified and I have correctly modelled those (see >>>>> image below). However, at this Tyr, I don't see an anomalous signal. >>>>> >>>>> [image: 4.png] >>>>> >>>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne <g...@globalphasing.com> >>>>> wrote: >>>>> >>>>> > Dear Misba, >>>>> > >>>>> > A wild guess: have you considered the possibility that this extra >>>>> > density could be a cacodylate adduct? Cacodylate is well known to react >>>>> > with >>>>> > thiols - see >>>>> > >>>>> > >>>>> > [https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D&reserved=0) >>>>> > >>>>> > Here the chemistry is different but you never know. If your data are >>>>> > redundant enough that you have good anomalous completeness, and were >>>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to >>>>> > compute an anomalous difference Fourier and check for the presence of a >>>>> > peak >>>>> > at the same location as the highest one in your ordinary difference map. >>>>> > >>>>> > Only a wild guess, though ... . >>>>> > >>>>> > >>>>> > With best wishes, >>>>> > >>>>> > Gerard. >>>>> > >>>>> > -- >>>>> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote: >>>>> > > Placing a water molecule satisfies most of the density and forms nice >>>>> > > H-bonds but there is still some residual density left (8.6 and 5.6 >>>>> > > rmsd). >>>>> > > >>>>> > > Best >>>>> > > Misbha >>>>> > > [image: 3.png] >>>>> > > >>>>> > > >>>>> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer >>>>> > > <k.futte...@bham.ac.uk> >>>>> > > wrote: >>>>> > > >>>>> > > > Looks more like water molecules. Phosphorylation would give a much >>>>> > bigger >>>>> > > > peak, and shape of density does not fit either. I don't think this >>>>> > > > is a >>>>> > > > covalent modification. Model some water molecules and see what the >>>>> > > > distances are and what difference density is left. >>>>> > > > >>>>> > > > >>>>> > > > Klaus >>>>> > > > >>>>> > > > >>>>> > > > ======================================================= >>>>> > > > Klaus Fütterer, PhD >>>>> > > > Reader in Structural Biology >>>>> > > > >>>>> > > > >>>>> > > > School of Biosciences >>>>> > > > LES College Email: >>>>> > > > k.futte...@bham.ac.uk >>>>> > > > University of Birmingham Phone: +44 - 121 - 414 >>>>> > > > 5895 >>>>> > > > Birmingham, B15 2TT, UK (voice mail messages >>>>> > > > will forward to my email inbox) >>>>> > > > >>>>> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm. >>>>> > > > >>>>> > > > >>>>> > > > ======================================================= >>>>> > > > ------------------------------ >>>>> > > > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of >>>>> > > > misba.ah...@gmail.com <misba.ah...@gmail.com> >>>>> > > > *Sent:* 29 January 2022 09:45:24 >>>>> > > > *To:* CCP4BB@JISCMAIL.AC.UK >>>>> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification >>>>> > > > >>>>> > > > Hi Tom, >>>>> > > > The protein was expressed in E Coli. >>>>> > > > >>>>> > > > Best >>>>> > > > Misbha >>>>> > > > >>>>> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) < >>>>> > > > tom.p...@csiro.au> wrote: >>>>> > > > >>>>> > > >> Hello Misba, >>>>> > > >> >>>>> > > >> Doesn't quite look like a phosphate, maybe O-sulfation? >>>>> > > >> Maybe just as important as the buffer and crystallisation >>>>> > > >> conditions >>>>> > > >> would be how it was expressed? Insect cells? >>>>> > > >> >>>>> > > >> Best of luck, tom >>>>> > > >> >>>>> > > >> Tom Peat, PhD >>>>> > > >> >>>>> > > >> Biomedical Program, CSIRO >>>>> > > >> tom.p...@csiro.au >>>>> > > >> >>>>> > > >> ------------------------------ >>>>> > > >> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of >>>>> > Misba >>>>> > > >> Ahmad <misba.ah...@gmail.com> >>>>> > > >> *Sent:* Saturday, January 29, 2022 8:12 PM >>>>> > > >> *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> >>>>> > > >> *Subject:* [ccp4bb] Help with interpreting Tyrosine modification >>>>> > > >> >>>>> > > >> Hi all, >>>>> > > >> I am trying to interpret this strong difference density peak (11.33 >>>>> > rmsd) >>>>> > > >> that shows up on the tyrosine residue. Any help would be greatly >>>>> > > >> appreciated. >>>>> > > >> >>>>> > > >> Purification buffer: 20mM HEPES pH 7.5, 250mM NaCl, 1mM TCEP, 5mM >>>>> > > >> DTT >>>>> > > >> Crystallisation condition: Sodium propionate, Sodium cacodylate, >>>>> > BIS-TRIS >>>>> > > >> propane, PEG 1500 >>>>> > > >> >>>>> > > >> Best >>>>> > > >> Misbha >>>>> > > >> [image: Picture1.png] >>>>> > > >> [image: Picture2.png] >>>>> > > >> >>>>> > > >> ------------------------------ >>>>> > > >> >>>>> > > >> To unsubscribe from the CCP4BB list, click the following link: >>>>> > > >> [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) >>>>> > > >> >>>>> > > > >>>>> > > > ------------------------------ >>>>> > > > >>>>> > > > To unsubscribe from the CCP4BB list, click the following link: >>>>> > > > [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) >>>>> > > > >>>>> > > >>>>> > > ######################################################################## >>>>> > > >>>>> > > To unsubscribe from the CCP4BB list, click the following link: >>>>> > > [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) >>>>> > > >>>>> > > This message was issued to members of >>>>> > > [www.jiscmail.ac.uk/CCP4BB](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UDM70dMM3pQKpjpQgRps1vp4%2FRB3gEj%2FfxYhg%2B08HUM%3D&reserved=0), >>>>> > > a >>>>> > mailing list hosted by >>>>> > [www.jiscmail.ac.uk](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LH6YB0%2BSFDbpm8tgesEoFFVfJySF2892PTh7Xz9bbSU%3D&reserved=0), >>>>> > terms & conditions are >>>>> > available at >>>>> > [https://www.jiscmail.ac.uk/policyandsecurity/](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=OejFfw7zh8MfsDHiihLqtgumdwBaY%2B3QpqFHWf369AQ%3D&reserved=0) >>>>> > >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) >>>> >>>> This message was issued to members of >>>> [www.jiscmail.ac.uk/CCP4BB](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=UDM70dMM3pQKpjpQgRps1vp4%2FRB3gEj%2FfxYhg%2B08HUM%3D&reserved=0), >>>> a mailing list hosted by >>>> [www.jiscmail.ac.uk](https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LH6YB0%2BSFDbpm8tgesEoFFVfJySF2892PTh7Xz9bbSU%3D&reserved=0), >>>> terms & conditions are available at >>>> [https://www.jiscmail.ac.uk/policyandsecurity/](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=OejFfw7zh8MfsDHiihLqtgumdwBaY%2B3QpqFHWf369AQ%3D&reserved=0) >>> >>> --------------------------------------------------------------- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) >>> >>> --------------------------------------------------------------- >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> [https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=En0%2FQm6ab6N1tngcVea7xBP7vJFEzwFQCEVcIZqCbQg%3D&reserved=0) > > --------------------------------------------------------------- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
